Ectonucleotide pyrophosphate-phosphodiesterase (enpp) conjugates and uses thereof

Abstract

Disclosed herein are ecto-nucleotide pyrophosphatase/phosphodiesterase (ENPP) complexes and synthetic molecules that interact with an ENPP protein. In some embodiments, also disclosed herein are modified ENPP polypeptides in complex with a synthetic molecule described herein.

What is claimed is: 
     
         1 . An ecto-nucleotide pyrophosphatase/phosphodiesterase (ENPP) complex having a synthetic molecule in contact with at least one residue at an amino acid position corresponding to amino acid residues D218, T256, F257, N277, L290, K295, W322, P323, D326, Y340, Y371, D376, H380, D423, H424, or H535 as set forth in SEQ ID NO: 1, wherein the synthetic molecule is not a hydrolysis product of a nucleoside triphosphate. 
     
     
         2 . The ENPP-molecule complex of  claim 1 , wherein the molecule is in contact with at least one residue at an amino acid position corresponding to:
 amino acid residues D218, T256, F257, N277, W322, D326, Y340, D376, H380, D423, H424, or H535 as set forth in SEQ ID NO: 1;   amino acid residues T256, F257, N277, W322, P323, D326, Y340, or Y371 as set forth in SEQ ID NO: 1;   amino acid residues T256, F257, N277, W322, P323, Y340, or Y371 as set forth in SEQ ID NO: 1;   amino acid residues F257, W322, D326, or Y340 as set forth in SEQ ID NO: 1;   amino acid residues F257 or Y340 as set forth in SEQ ID NO: 1; or   amino acid residues D326 or W322 as set forth in SEQ ID NO: 1.   
     
     
         3 . The ENPP-molecule complex of  claim 1 , wherein the synthetic molecule has a structure represented by Formula (I), or a pharmaceutically acceptable salt, solvate, or stereoisomer thereof: 
       
         
           
           
               
               
           
         
         wherein 
         L is —(CR 3 R 4 ) n —; 
         X is —N— or —CH—; 
         Ring A is
 (a) an optionally substituted heteroaryl that is not quinazolinyl or pyrimidyl; or 
 (b) an optionally substituted heterocycloalkyl; or 
 (c) a ring selected from 
 
       
       
         
           
           
               
               
           
         
         each R 1  is independently hydrogen, halogen, —CN, —OR 11 , —SR 11 , —S(═O)R 10 , —NO 2 , —NR 11 R 12 , —S(═O) 2 R 10 , —NR 11 S(═O) 2 R 10 , —S(═O) 2 NR 11 R 12 , —C(═O)R 10 , —OC(═O)R 10 , —C(═O)OR 11 , —OC(═O)OR 11 , —C(═O)NR 11 R 12 , —OC(═O)NR 11 R 12 , —NR 11 C(═O)NR 11 R 12 , —NR 11 C(═O)R 10 , —NR 11 C(═O)OR 11 , optionally substituted C 1 -C 6  alkyl, optionally substituted C 1 -C 6  heteroalkyl, optionally substituted C 2 -C 6  alkenyl, optionally substituted C 2 -C 6  alkynyl, optionally substituted cycloalkyl, optionally substituted (C 1 -C 6  alkyl)cycloalkyl, optionally substituted heterocycloalkyl, optionally substituted (C 1 -C 6  alkyl)heterocycloalkyl, optionally substituted aryl, optionally substituted (C 1 -C 6  alkyl)aryl, optionally substituted heteroaryl, and optionally substituted (C 1 -C 6  alkyl)heteroaryl; 
         or two R 1  on the same carbon are taken together to form an oxo; 
         R 2a  is hydrogen, —SR 11 , —S(═O)R 10 , —S(═O) 2 R 10 , —S(═O) 2 NR 11 R 12 , —C(═O)R 10 , —C(═O)NR 11 R 12 , optionally substituted C 1 -C 6  alkyl, optionally substituted C 1 -C 6  heteroalkyl, optionally substituted C 2 -C 6  alkenyl, optionally substituted C 2 -C 6  alkynyl, optionally substituted cycloalkyl, optionally substituted (C 1 -C 6  alkyl)cycloalkyl, optionally substituted heterocycloalkyl, optionally substituted (C 1 -C 6  alkyl)heterocycloalkyl, optionally substituted aryl, optionally substituted (C 1 -C 6  alkyl)aryl, optionally substituted heteroaryl, or optionally substituted (C 1 -C 6  alkyl)heteroaryl; 
         each R 3  and R 4  are independently hydrogen, halogen, —CN, —OR 11 , —SR 11 , —S(═O)R 10 , —NO 2 , —NR 11 R 12 , —S(═O) 2 R 10 , —NR 11 S(═O) 2 R 10 , —S(═O) 2 NR 11 R 12 , —C(═O)R 10 , —OC(═O)R 10 , —C(═O)OR 11 , —OC(═O)OR 11 , —C(═O)NR 11 R 12 , —OC(═O)NR 11 R 12 , —NR 11 C(═O)NR 11 R 12 , —NR 11 C(═O)R 10 , —NR 11 C(═O)OR 11 , optionally substituted C 1 -C 6  alkyl, optionally substituted C 1 -C 6  heteroalkyl, optionally substituted C 2 -C 6  alkenyl, or optionally substituted C 2 -C 6  alkynyl; 
         or R 3  and R 4  on the same carbon are taken together to form an oxo; 
         R 5  is halogen, —CN, —OR 11 , —SR 11 , —S(═O)R 10 , —NO 2 , —NR 11 R 12 , —S(═O) 2 R 10 , —NR 11 S(═O) 2 R 10 , —S(═O) 2 NR 11 R 12 , —C(═O)R 10 , —OC(═O)R 10 , —C(═O)OR 11 , —OC(═O)OR 11 , —C(═O)NR 11 R 12 , —OC(═O)NR 11 R 12 , —NR 11 C(═O)NR 11 R 12 , —NR 11 C(═O)R 10 , —NR 11 C(═O)OR 11 , optionally substituted C 1 -C 6  heteroalkyl, optionally substituted C 2 -C 6  alkynyl, optionally substituted cycloalkyl, optionally substituted (C 1 -C 6  alkyl)cycloalkyl, optionally substituted heterocycloalkyl, optionally substituted (C 1 -C 6  alkyl)heterocycloalkyl, optionally substituted aryl, optionally substituted (C 1 -C 6  alkyl)aryl, optionally substituted heteroaryl, or optionally substituted (C 1 -C 6  alkyl)heteroaryl; 
         R 6  is hydrogen, halogen, —CN, —OR 11 , —SR 11 , —S(═O)R 10 , —NO 2 , —NR 11 R 12 , —S(═O) 2 R 10 , —NR 11 S(═O) 2 R 10 , —S(═O) 2 NR 11 R 12 , —C(═O)R 10 , —OC(═O)R 10 , —C(═O)OR 11 , —OC(═O)OR 11 , —C(═O)NR 11 R 12 , —OC(═O)NR 11 R 12 , —NR 11 C(═O)NR 11 R 12 , —NR 11 C(═O)R 10 , —NR 11 C(═O)OR 11 , optionally substituted C 1 -C 6  alkyl, optionally substituted C 1 -C 6  heteroalkyl, optionally substituted C 2 -C 6  alkenyl, optionally substituted C 2 -C 6  alkynyl, optionally substituted cycloalkyl, optionally substituted (C 1 -C 6  alkyl)cycloalkyl, optionally substituted heterocycloalkyl, optionally substituted (C 1 -C 6  alkyl)heterocycloalkyl, optionally substituted aryl, optionally substituted (C 1 -C 6  alkyl)aryl, optionally substituted heteroaryl, or optionally substituted (C 1 -C 6  alkyl)heteroaryl; provided that R 6  is not substituted imidazolyl; 
         R 7  is hydrogen, halogen, —CN, —OR 11 , —SR 11 , —S(═O)R 10 , —NO 2 , —NR 11 R 12 , —S(═O) 2 R 10 , —NR 11 S(═O) 2 R 10 , —S(═O) 2 NR 11 R 12 , —C(═O)R 10 , —OC(═O)R 10 , —C(═O)OR 11 , —OC(═O)OR 11 , —C(═O)NR 11 R 12 , —OC(═O)NR 11 R 12 , —NR 11 C(═O)NR 11 R 12 , —NR 11 C(═O)R 10 , —NR 11 C(═O)OR 11 , optionally substituted C 1 -C 6  alkyl, optionally substituted C 1 -C 6  heteroalkyl, optionally substituted C 2 -C 6  alkenyl, optionally substituted C 2 -C 6  alkynyl, optionally substituted cycloalkyl, optionally substituted (C 1 -C 6  alkyl)cycloalkyl, optionally substituted heterocycloalkyl, optionally substituted (C 1 -C 6  alkyl)heterocycloalkyl, optionally substituted (C 1 -C 6  alkyl)aryl, optionally substituted heteroaryl, or optionally substituted (C 1 -C 6  alkyl)heteroaryl; provided that R 7  is not substituted imidazolyl; 
         each R a  is independently hydrogen, halogen, —CN, —OR 11 , —SR 11 , —S(═O)R 10 , —NO 2 , —NR 11 R 12 , —S(═O) 2 R 10 , —NR 11 S(═O) 2 R 10 , —S(═O) 2 NR 11 R 12 , —C(═O)R 10 , —OC(═O)R 10 , —C(═O)OR 11 , —OC(═O)OR 11 , —C(═O)NR 11 R 12 , —OC(═O)NR 11 R 12 , —NR 11 C(═O)NR 11 R 12 , —NR 11 C(═O)R 10 , —NR 11 C(═O)OR 11 , optionally substituted C 1 -C 6  alkyl, optionally substituted C 1 -C 6  heteroalkyl, optionally substituted C 2 -C 6  alkenyl, optionally substituted C 2 -C 6  alkynyl, optionally substituted cycloalkyl, optionally substituted (C 1 -C 6  alkyl)cycloalkyl, optionally substituted heterocycloalkyl, optionally substituted (C 1 -C 6  alkyl)heterocycloalkyl, optionally substituted aryl, optionally substituted (C 1 -C 6  alkyl)aryl, optionally substituted heteroaryl, or optionally substituted (C 1 -C 6  alkyl)heteroaryl; 
         each R 10  is optionally substituted C 1 -C 6  alkyl, optionally substituted C 2 -C 6  alkenyl, optionally substituted C 2 -C 6  alkynyl, optionally substituted cycloalkyl, optionally substituted heterocycloalkyl, optionally substituted aryl, or optionally substituted heteroaryl; 
         each R 11  and R 12  are each independently hydrogen, optionally substituted C 1 -C 6  alkyl, optionally substituted C 2 -C 6  alkenyl, optionally substituted C 2 -C 6  alkynyl, optionally substituted cycloalkyl, optionally substituted heterocycloalkyl, optionally substituted aryl, or optionally substituted heteroaryl; 
         or R 11  and R 12  are taken together with the nitrogen atom to which they are attached to form an optionally substituted heterocycloalkyl;
 n is 1-4; 
 p is 1-4; 
 p1 is 0 or 1; 
 q1 is 1-4; and 
 q2 is 1-2. 
 
       
     
     
         4 . The ENPP-molecule complex of  claim 3 , wherein R 2a  is hydrogen. 
     
     
         5 . The ENPP-molecule complex of  claim 3 , wherein: L is —(CR 3 R 4 ) n —; n is 2; and each R 3  and R 4  are independently hydrogen or halogen. 
     
     
         6 . The ENPP-molecule complex of  claim 3 , wherein X is —CH—. 
     
     
         7 . The ENPP-molecule complex of  claim 3 , wherein X is —N—. 
     
     
         8 . The ENPP-molecule complex of  claim 3 , wherein Ring A is selected from: 
       
         
           
           
               
               
           
         
       
       and
 each R b  is independently hydrogen, —SR 11 , —S(═O)R 10 , —S(═O) 2 R 10 , —S(═O) 2 NR 11 R 12 , —C(═O)R 10 , —C(═O)NR 11 R 12 , optionally substituted C 1 -C 6  alkyl, optionally substituted C 1 -C 6  heteroalkyl optionally substituted C 2 -C 6  alkenyl, optionally substituted C 2 -C 6  alkynyl, optionally substituted cycloalkyl, optionally substituted (C 1 -C 6  alkyl)cycloalkyl, optionally substituted heterocycloalkyl, optionally substituted (C 1 -C 6  alkyl)heterocycloalkyl, optionally substituted aryl, optionally substituted (C 1 -C 6  alkyl)aryl, optionally substituted heteroaryl, or optionally substituted (C 1 -C 6  alkyl)heteroaryl. 
 
     
     
         9 . The ENPP-molecule complex of  claim 3 , wherein Ring A is 
       
         
           
           
               
               
           
         
       
     
     
         10 . The ENPP-molecule complex of  claim 9 , wherein each R a  is independently hydrogen, halogen, —CN, —OR 11 , optionally substituted C 1 -C 6  alkyl, or optionally substituted C 1 -C 6  heteroalkyl; and q1 is 2 or 3. 
     
     
         11 . The ENPP-molecule complex of  claim 9 , wherein R 5  is halogen, —CN, —OR 11 , —NR 11 R 12 , —C(═O)OR 11 , —NR 11 C(═O)R 10 , optionally substituted C 1 -C 6  heteroalkyl, optionally substituted cycloalkyl, optionally substituted heterocycloalkyl, optionally substituted aryl, or optionally substituted heteroaryl. 
     
     
         12 . The ENPP-molecule complex of  claim 3 , wherein Ring A is 
       
         
           
           
               
               
           
         
       
     
     
         13 . The ENPP-molecule complex of  claim 12 , wherein each R a  is independently hydrogen, halogen, —CN, —OR 11 , optionally substituted C 1 -C 6  alkyl, or optionally substituted C 1 -C 6  heteroalkyl; and q2 is 1. 
     
     
         14 . The ENPP-molecule complex of  claim 12 , wherein R 7  is hydrogen, halogen, —CN, —OR 11 , —NR 11 R 12 , —NR 11 C(═O)R 10 , —C(═O)NR 11 R 12 , optionally substituted C 1 -C 6  alkyl, optionally substituted C 1 -C 6  heteroalkyl, optionally substituted cycloalkyl, optionally substituted heterocycloalkyl, optionally substituted aryl, or optionally substituted heteroaryl; provided that R is not substituted imidazolyl. 
     
     
         15 . The ENPP-molecule complex of  claim 3 , wherein Ring A is 
       
         
           
           
               
               
           
         
       
     
     
         16 . The ENPP-molecule complex of  claim 15 , wherein each R a  is independently hydrogen, halogen, —CN, —OR 11 , optionally substituted C 1 -C 6  alkyl, or optionally substituted C 1 -C 6  heteroalkyl; and q2 is 1. 
     
     
         17 . The ENPP-molecule complex of  claim 15 , wherein R 6  is hydrogen, halogen, —CN, —OR 11 , —NR 11 R 12 , —NR 11 C(═O)R 10 , optionally substituted C 1 -C 6  alkyl, optionally substituted C 1 -C 6  heteroalkyl, optionally substituted cycloalkyl, optionally substituted heterocycloalkyl, optionally substituted aryl, or optionally substituted heteroaryl; provided that R 6  is not substituted imidazolyl. 
     
     
         18 . The ENPP-molecule complex of  claim 1 , wherein the synthetic molecule has a structure represented by Formula (III), or a pharmaceutically acceptable salt, solvate, or stereoisomer thereof: 
       
         
           
           
               
               
           
         
         wherein 
         Y is —O— or —NR 20 —; 
         L 2  is a bond or —(CR 21 R 22 ) n2 —; 
         W 1  and W 2  are independently N or CR a ; provided that at least one of W 1  or W 2  is N; 
         Ring C is aryl, heteroaryl, cycloalkyl, or heterocycloalkyl; 
         each R 23  is independently hydrogen, halogen, —CN, —OR 11 , —SR 11 , —S(═O)R 10 , —NO 2 , —NR 11 R 12 , —S(═O) 2 R 10 , —NR 11 S(═O) 2 R 10 , —S(═O) 2 NR 11 R 12 , —C(═O)R 10 , —OC(═O)R 10 , —C(═O)OR 11 , —OC(═O)OR 11 , —C(═O)NR 11 R 12 , —OC(═O)NR 11 R 12 , —NR 11 C(═O)NR 11 R 12 , —NR 11 C(═O)R 10 , —NR 11 C(═O)OR 11 , optionally substituted C 1 -C 6  alkyl, optionally substituted C 1 -C 6  heteroalkyl, optionally substituted C 2 -C 6  alkenyl, optionally substituted C 2 -C 6  alkynyl, optionally substituted cycloalkyl, optionally substituted (C 1 -C 6  alkyl)cycloalkyl, optionally substituted heterocycloalkyl, optionally substituted (C 1 -C 6  alkyl)heterocycloalkyl, optionally substituted aryl, optionally substituted (C 1 -C 6  alkyl)aryl, optionally substituted heteroaryl, or optionally substituted (C 1 -C 6  alkyl)heteroaryl; 
         R 2c  is hydrogen, —SR 11 , —S(═O)R 10 , —S(═O) 2 R 10 , —S(═O) 2 NR 11 R 12 , —C(═O)R 10 , —C(═O)NR 11 R 12 , optionally substituted C 1 -C 6  alkyl, optionally substituted C 1 -C 6  heteroalkyl, optionally substituted C 2 -C 6  alkenyl, optionally substituted C 2 -C 6  alkynyl, optionally substituted cycloalkyl, optionally substituted (C 1 -C 6  alkyl)cycloalkyl, optionally substituted heterocycloalkyl, optionally substituted (C 1 -C 6  alkyl)heterocycloalkyl, optionally substituted aryl, optionally substituted (C 1 -C 6  alkyl)aryl, optionally substituted heteroaryl, or optionally substituted (C 1 -C 6  alkyl)heteroaryl; 
         R 20  is hydrogen, —SR 11 , —S(═O)R 10 , —S(═O) 2 R 10 , —S(═O) 2 NR 11 R 12 , —C(═O)R 10 , —C(═O)NR 11 R 12 , optionally substituted C 1 -C 6  alkyl, optionally substituted C 1 -C 6  heteroalkyl, optionally substituted C 2 -C 6  alkenyl, optionally substituted C 2 -C 6  alkynyl, optionally substituted cycloalkyl, optionally substituted (C 1 -C 6  alkyl)cycloalkyl, optionally substituted heterocycloalkyl, optionally substituted (C 1 -C 6  alkyl)heterocycloalkyl, optionally substituted aryl, optionally substituted (C 1 -C 6  alkyl)aryl, optionally substituted heteroaryl, or optionally substituted (C 1 -C 6  alkyl)heteroaryl; 
         each R 21  and R 22  are independently hydrogen, halogen, —CN, —OR 11 , —SR 11 , —S(═O)R 10 , —NO 2 , —NR 11 R 12 , —S(═O) 2 R 10 , —NR 11 S(═O) 2 R 10 , —S(═O) 2 NR 11 R 12 , —C(═O)R 10 , —OC(═O)R 10 , —C(═O)OR 11 , —OC(═O)OR 11 , —C(═O)NR 11 R 12 , —OC(═O)NR 11 R 12 , —NR 11 C(═O)NR 11 R 12 , —NR 11 C(═O)R 10 , —NR 11 C(═O)OR 11 , optionally substituted C 1 -C 6  alkyl, optionally substituted C 1 -C 6  heteroalkyl, optionally substituted C 2 -C 6  alkenyl, or optionally substituted C 2 -C 6  alkynyl; 
         or R 21  and R 22  on the same carbon are taken together to form an oxo; 
         each R a  is independently hydrogen, halogen, —CN, —OR 11 , —SR 11 , —S(═O)R 10 , —NO 2 , —NR 11 R 12 , —S(═O) 2 R 10 , —NR 11 S(═O) 2 R 10 , —S(═O) 2 NR 11 R 12 , —C(═O)R 10 , —OC(═O)R 10 , —C(═O)OR 11 , —OC(═O)OR 11 , —C(═O)NR 11 R 12 , —OC(═O)NR 11 R 12 , —NR 11 C(═O)NR 11 R 12 , —NR 11 C(═O)R 10 , —NR 11 C(═O)OR 11 , optionally substituted C 1 -C 6  alkyl, optionally substituted C 1 -C 6  heteroalkyl, optionally substituted C 2 -C 6  alkenyl, optionally substituted C 2 -C 6  alkynyl, optionally substituted cycloalkyl, optionally substituted (C 1 -C 6  alkyl)cycloalkyl, optionally substituted heterocycloalkyl, optionally substituted (C 1 -C 6  alkyl)heterocycloalkyl, optionally substituted aryl, optionally substituted (C 1 -C 6  alkyl)aryl, optionally substituted heteroaryl, or optionally substituted (C 1 -C 6  alkyl)heteroaryl; 
         each R 10  is optionally substituted C 1 -C 6  alkyl, optionally substituted C 2 -C 6  alkenyl, optionally substituted C 2 -C 6  alkynyl, optionally substituted cycloalkyl, optionally substituted heterocycloalkyl, optionally substituted aryl, or optionally substituted heteroaryl; 
         each R 11  and R 12  are each independently hydrogen, optionally substituted C 1 -C 6  alkyl, optionally substituted C 2 -C 6  alkenyl, optionally substituted C 2 -C 6  alkynyl, optionally substituted cycloalkyl, optionally substituted heterocycloalkyl, optionally substituted aryl, or optionally substituted heteroaryl; 
         or R 11  and R 12  are taken together with the nitrogen atom to which they are attached to form an optionally substituted heterocycloalkyl;
 t is 1-4; 
 n2 is 1 or 2; and 
 u is 1-4. 
 
       
     
     
         19 . The ENPP-molecule complex of  claim 18 , wherein W 1  and W 2  are N. 
     
     
         20 . The ENPP-molecule complex of  claim 18 , each R a  is independently hydrogen, halogen, —CN, —OR 11 , —NR 11 R 12 , —C(═O)OR 11 , —OC(═O)OR 11 , —C(═O)NR 11 R 12 , optionally substituted C 1 -C 6  alkyl, optionally substituted C 1 -C 6  heteroalkyl, optionally substituted cycloalkyl, or optionally substituted heterocycloalkyl; and u is 1-3. 
     
     
         21 . The ENPP-molecule complex of  claim 18 , wherein each R 23  is independently hydrogen, halogen, or optionally substituted C 1 -C 6  alkyl. 
     
     
         22 . The ENPP-molecule complex of  claim 18 , wherein L 2  is a bond. 
     
     
         23 . The ENPP-molecule complex of  claim 18 , wherein L 2  is —(CR 21 R 22 ) n2 —; n2 is 1 or 2; and
 each R 21  and R 22  are independently hydrogen or halogen 
 
     
     
         24 . The ENPP-molecule complex of  claim 18 , wherein R 2c  is hydrogen. 
     
     
         25 . The ENPP-molecule complex of  claim 18 , wherein Ring C is a 6-membered aryl. 
     
     
         26 . The ENPP-molecule complex of  claim 16 , wherein Ring C is a 5- or 6-membered heteroaryl. 
     
     
         27 . The ENPP-molecule complex of  claim 1 , wherein the contact comprises covalent interaction, non-covalent interaction, or a combination thereof. 
     
     
         28 . The ENPP-molecule complex of  claim 1 , wherein the contact comprises hydrogen bonding, hydrophobic interaction, ionic interaction, Van der Waals interaction, electrostatic interaction, pi bonding, or a combination thereof. 
     
     
         29 . The ENPP-molecule complex of  claim 1 , wherein the ecto-nucleotide pyrophosphatase/phosphodiesterase is ecto-nucleotide pyrophosphatase/phosphodiesterase 1 (ENPP1). 
     
     
         30 . The ENPP-molecule complex of  claim 1 , wherein the hydrolysis product is AMP, TMP, GMP, or CMP.